SeqVarTools (version 1.10.0)

isSNV: Flag single nucleotide variants

Description

Flag single nucleotide variants

Usage

"isSNV"(x, biallelic=TRUE)

Arguments

x

A SeqVarGDSClass object with VCF data.

biallelic

A logical indicating whether only biallelic SNVs are considered.

Value

A logical vector indicating which variants are SNVs.

Details

If biallelic=TRUE, a variant is considered a single nucleotide variant (SNV) if there is one reference allele and one alternate allele, each one base in length. If biallelic=FALSE, there may be multiple alternate alleles, each one base in length.

Setting biallelic=TRUE is considerably faster for large data sets.

See Also

SeqVarGDSClass, allele-methods, applyMethod

Examples

gds <- seqOpen(seqExampleFileName("gds"))
table(isSNV(gds))
seqClose(gds)